Objective To investigate the epidemic situation of hemorrhagic fever with renal syndrome (HFRS) in Fujian province, China and to provide a scientific basis for the prevention and control of this disease. Methods The data on the epidemic situation of HFRS in Fujian province were subjected to statistical analysis. Rodents were captured using cages at night. The density of captured rodents was calculated, and their species were identified. Hantavirus antigen was detected and identified from rodent lungs by indirect immunofluorescence assay. Results A total of 259 cases of HFRS were reported in Fujian in 2011, with an incidence of 0.70/105. The cases were distributed in 64 counties, county-level cities, or districts, particularly in Nanping, Ningde, Fuzhou, and Quanzhou. The incidence of HFRS was the highest in Songxi county and Zhouning county. The surveillance of rodents showed that the mean density of rodents was 8.22% indoors, and Rattus norvegicus, which carried Soul virus (typeⅡ), was the dominant species. In the mixed epidemic area, the mean density of rodents was 6.53% in the field, and R. fulvescens was the dominant species, followed by Apodemus agrarius, which carried Hantaan virus (type Ⅰ). HFRS virus antigen was first detected from R. norvegicus in Dehua county. Conclusion R. norvegicus is still the main host animal of HFRS in Fujian, and A. agrarius is the main host of HFRS in the field of mixed epidemic area in the northeastern area of Fujian. In 2011, the incidence of HFRS in Fujian increased significantly, especially in Songxi county and Zhouning county. Rodent control should be well performed, and HFRS bivalent vaccine should be widely used among the high-risk population, so as to reduce the incidence and prevent the outbreak of HFRS.